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International audience; Correctly delimiting species and populations is a prerequisite for studies of connectivity, adaptation and conservation. Genomic data are particularly useful to test for species differentiation for organisms with few informative morphological characters or low discrimination of cytoplasmic markers, as in Scleractinians. Here we applied Restriction site Associated DNA sequencing (RADsequencing) to the study of species differentiation and genetic structure in populations of Pocillopora spp. from Oman and French Polynesia, with the objectives to test species hypotheses, and to study the genetic structure among sampling sites within species. We focused here on coral colonies morphologically similar to P. acuta (damicornis type β). We tested the impact of different filtering strategies on the stability of the results. The main genetic differentiation was observed between samples from Oman and French Polynesia. These samples corresponded to different previously defined primary species hypotheses (PSH), i.e. PSHs 12 and 13 in Oman, and PSH 5 in French Polynesia. In Oman, we did not observe any clear differentiation between the two putative species PSH 12 and 13, nor between sampling sites. In French Polynesia, where a single species hypothesis was studied, there was no differentiation between sites. Our analyses allowed the identification of clonal lineages in Oman and French Polynesia. The impact of clonality on genetic diversity is discussed in light of individual-based simulations.

This is an extended version of Figure S2 from the study The War of Corals by Mohsen Kayal & Mehdi Adjeroud. A preprint of the study is available at:https://doi.org/10.1101/2021.12.06.471466 The manuscript is presently under revision for publication in Royal Society Open Science.

Extended Appendix 1 from the studyThe War of Corals by Mohsen Kayal & Mehdi Adjeroud oncoral competitive interactions under changing reef environments.Original posts fromhttps://www.instagram.com/m.o.k.a.y/ Study preprint:https://doi.org/10.1101/2021.12.06.471466 Manuscript in revision for publication in Royal Society Open Science &nbsp

Este artículo contiene 11 páginas, 5 figuras, 1 tabla., Isolated coral reef habitats are unique systems to study the natural dynamics of coral traits and their natural acclimatization, adaptation, and recovery from globalscale stressors such as thermally induced bleaching events. This study evaluates the spatial and temporal changes in coral community attributes (diversity, live cover, and coral assemblage structure) over 14 years (2005–2019) at Clipperton, an extremely remote Eastern Tropical Pacific (ETP) atoll. The atoll exhibited overall high coral cover (~ 50–60%) dominated by massive species (Porites spp.), yet we observed large variation (44–56%) in coral community attributes among survey years (2005, 2016, 2019) with depth explaining most of the variation. Live coral cover increased in 2019 after a severe thermal stress event (El Niño, 2015– 2016) and many tropical cyclones, which also caused a shift in assemblage structure from branching Pocillopora to massive Porites in the shallower reef zones, resulting in a less well-defined depth gradient. These changes in coral assemblage structure may have long-term effects on the configuration of the physical reef framework of the well-conserved coral reef ecosystems at Clipperton and consequently may alter the ecological functionality of one of the most important biogeographic stepping stones in the central Pacific and ETP regions., The present work was supported by Consejo Nacional de Ciencia y Tecnología (CONACYT) postdoctoral fellowship (CVU 410380) to JJATL. We thank the government of France, The Embassy of France in Mexico, Ministère Des Outre-Mer, the Mexican government, Centro de Investigación de la Isla Observatorio del Medio Ambiente (CRIOBE USR3278 EPHE-CNRS-UPVD), Instituto Nacional de Pesca y Acuacultura (INAPESCA), and the oceanographic research vessel Jorge Carranza Fraser from INAPESCA and also thank the Haut Commissariat de la République en Polynésie française for permission to perform this research at Clipperton Atoll (CITES permit no. FR1998700218-E).

Coral reefs of Madagascar have been impacted by numerous disturbances, and Marine Protected Areas (MPAs) have been established to limit this decline. Studies of Madagascar's reefs began in the 1960s, but most of the work has been done at the local scale and with different methodologies. Furthermore, resilience capacities remain largely undocumented in Madagascar. While the positive effect of MPAs on coastal fisheries has been demonstrated, the effect on corals has not been rigorously addressed. In this context, the main objective of this Thesis was to examine the effect of MPAs on the spatial structure, regulation processes and recovery potential of coral assemblages in Madagascar. A total of 18 study stations were distributed in 3 regions: Masoala in the northeast, Nosy-Be in the northwest and Salary Nord in the southwest. In each region, 3 stations were established in fished areas and three in unfished areas of MPAs. Three 10 m2 belt-transects were surveyed at each station between March and October 2020, to determine taxonomic composition, generic richness, Shannon diversity index, and abundance of adult and juvenile corals. The percent cover of corals, macroalgae, turf and crustose coralline algae (CCA) was estimated using three 10 m line transects. Cover of algae, herbivorous fish biomass (quantified using 250 m² belt-transects), substrate rugosity (visual assessment with 5 categories), fishing protection level, and geographic location were selected as explanatory variables of the structure of coral assemblages. Data on corals, algae and herbivorous fishes, coupled with those on thermal stress, allowed the calculation of a Recovery Index (RI) using the TOPSIS (Technique for Order Preference by Similarity to an Ideal Solution) method. The results showed a strong heterogeneity of all coral descriptors, at local and/or regional scales. At Masoala, high abundances, especially of stress-tolerant and competitive taxa, such as Acropora and Pocillopora, were recorded. Salary Nord was characterized by lower abundances, especially of competitive taxa. At Nosy-Be, a high diversity, abundance and coral cover was recorded. Generalized linear mixed effects models showed that this spatial structure was mainly influenced by herbivorous fishes, rugosity, and CCA cover. A positive effect of MPAs was also recorded for all descriptors except taxonomic composition. For most dominant genera, spatial variation of juveniles and adults was positively correlated, suggesting a "recruitment-limitation" model, though other taxa seem to be regulated by post-settlement events instead. Except for Porites, variation in juvenile density was not influenced by MPAs, whereas such an effect was found for adults of Acropora, Montipora, Seriatopora and Porites. A strong variation in RI was observed at local and regional scales, with a higher recovery potential in Masoala, probably related to less frequent temperature anomalies in this region. A positive effect of MPAs on RI was recorded in Nosy-Be, which harbors the oldest unfished areas of Madagascar (since 1966), and where control measures are more effective compared to other regions. Our results plead for a reinforcement of conservation measures, with actions focused on the protection during coral recruitment processes and on the recovery capacities. Important aspects include enforcement and the establishment of locally managed marine areas (LMMAs), which have proven effective in managing fisheries resources and appear to be a well-suited conservation action in Madagascar. This work represents a solid baseline to assist researchers and managers in monitoring the evolution of coral assemblages and making effective conservation decisions for Madagascar's coral reefs.; Les récifs coralliens de Madagascar ont été impactés par de nombreuses perturbations, et des Aires Marines Protégées (AMPs) ont été mises en place pour limiter ce déclin. L’étude de ces récifs a débuté dans les années 1960, mais la plupart des travaux ont concerné l’échelle locale et ont été réalisées avec des méthodologies différentes. Par ailleurs, les capacités de résilience restent peu documentées à Madagascar. Si l’effet positif des AMPs sur les pêcheries côtières a pu être mis en évidence, celui sur les coraux n’a pas été abordé. Dans ce contexte, cette thèse a eu pour objectif d’examiner l’effet des AMPs sur la structure spatiale, les processus de régulation et le potentiel de récupération des assemblages coralliens de Madagascar. Au total, 18 stations d’étude ont été réparties dans 3 régions : Masoala au nord-est, Nosy-Be au nord-ouest et Salary Nord au sud-ouest. À chaque région, 3 stations ont été mises en place dans des zones pêchées et 3 dans des zones non pêchées. Trois transect-couloirs de 10 m2 ont été prospectés à chaque station entre mars et octobre 2020, pour déterminer la composition taxonomique, la richesse générique, l’indice de diversité de Shannon, et l’abondance des colonies adultes et juvéniles. Le recouvrement en corail, en macroalgues, turf et algues calcaires encroûtantes, a été estimé à l’aide de 3 transects de 10 m de long. Le recouvrement en algues, la biomasse des poissons herbivores (quantifiée dans des transect-couloirs de 250 m²), la rugosité du substrat (estimée visuellement en 5 catégories), le niveau de protection (zones pêchées vs. AMPs), et la localisation géographique ont été retenus comme variables explicatives de la structure des assemblages coralliens. Un Indice de Récupération (RI) a été calculé avec la méthode TOPSIS (Technique for Order Preference by Similarity to an Ideal Solution), avec les données sur les coraux, algues et herbivores, et les stress thermiques. Une forte hétérogénéité des descripteurs coralliens a été mise en évidence aux échelles locale et/ou régionale. À Masoala, des abondances élevées, notamment des taxa tolérants aux stress et compétitifs, comme Acropora et Pocillopora, ont été enregistrées. Salary Nord est caractérisée par des abondances plus faibles, notamment des taxa compétitifs. À Nosy-Be, une forte diversité, abondance et couverture corallienne a été enregistrée. Des modèles linéaires généralisés ont montré que la structure spatiale était influencée par les herbivores, la rugosité, et la couverture en algues calcaires encroûtantes. Les résultats montrent un effet positif des AMPs sur tous les descripteurs à l’exception de la composition taxonomique. Pour la plupart des genres dominants, la variation spatiale de la densité des juvéniles et adultes est positivement corrélée, ce qui suggère la prépondérance d’un modèle de type « limitation par le recrutement ». À l’exception de Porites, la variation spatiale des juvéniles n’est pas influencée par les AMPs, alors qu’un tel effet a été mis en évidence pour les adultes d’Acropora, Montipora, Seriatopora et Porites. Une forte variation du RI a été observée, avec un potentiel de récupération plus élevé à Masoala, probablement en lien avec des anomalies de températures moins fréquentes dans cette région. L’effet positif des AMPs sur le RI n’a été observé qu’à Nosy-Be, où la mise en réserve est la plus ancienne (1966) et les mesures de contrôle plus efficaces qu’aux autres AMPs. Ces résultats plaident pour un renforcement des mesures de conservation, avec des actions focalisées sur le recrutement et les capacités de récupération des assemblages coralliens. Le contrôle de l’application des mesures est un aspect important, et la mise en place d’Aires Marines Gérées Localement paraît être une solution bien adaptée. Ce travail représente une base de référence solide pour suivre l’évolution des récifs de Madagascar, et pour aider les gestionnaires dans leur prise de décision pour leur conservation.